[2026-06-08T08:45:33] Launching Arriba 2.4.0
[2026-06-08T08:45:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:48] Reading chimeric alignments from 'aih-tih-sc-12b72b-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=12124764)
[2026-06-08T08:52:29] Marking multi-mapping alignments (marked=7796646)
[2026-06-08T08:52:34] Detecting strandedness (reverse)
[2026-06-08T08:52:34] Assigning strands to alignments 
[2026-06-08T08:52:37] Annotating alignments 
[2026-06-08T08:53:18] Filtering duplicates (remaining=4552204)
[2026-06-08T08:53:25] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=4243497)
[2026-06-08T08:53:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4243497)
[2026-06-08T08:53:30] Filtering viral contigs with expression lower than the top 5 (remaining=4243497)
[2026-06-08T08:53:35] Filtering viral contigs with less than 5% coverage (remaining=4243497)
[2026-06-08T08:53:38] Estimating fragment length (mate gap mean=-83.0838, mate gap stddev=27.3061, read length mean=119.884)
[2026-06-08T08:53:38] Filtering read-through fragments with a distance <=10000bp (remaining=3933471)
[2026-06-08T08:53:40] Filtering inconsistently clipped mates (remaining=3854054)
[2026-06-08T08:53:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3760799)
[2026-06-08T08:53:47] Filtering fragments with small insert size (remaining=3759605)
[2026-06-08T08:53:49] Filtering alignments with long gaps (remaining=3759605)
[2026-06-08T08:53:52] Filtering fragments with both mates in the same gene (remaining=3758576)
[2026-06-08T08:53:54] Filtering fusions arising from hairpin structures (remaining=3573733)
[2026-06-08T08:53:57] Filtering reads with a mismatch p-value <=0.01 (remaining=1489433)
[2026-06-08T08:54:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=602576)
[2026-06-08T08:54:16] Finding fusions and counting supporting reads (total=520261)
[2026-06-08T08:54:33] Merging adjacent fusion breakpoints (remaining=514162)
[2026-06-08T08:54:34] Filtering multi-mapping fusions by alignment score and read support (remaining=317106)
[2026-06-08T08:55:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:55:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=315894)
[2026-06-08T08:55:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=159285)
[2026-06-08T08:55:19] Filtering fusions with <2 supporting reads (remaining=17314)
[2026-06-08T08:55:20] Filtering fusions with an e-value >=0.3 (remaining=3804)
[2026-06-08T08:55:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3841)
[2026-06-08T08:55:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3772)
[2026-06-08T08:55:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3772)
[2026-06-08T08:55:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3490)
[2026-06-08T08:55:31] Searching for fusions with spliced split reads (remaining=3548)
[2026-06-08T08:55:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=2548)
[2026-06-08T08:55:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2538)
[2026-06-08T08:55:38] Searching for fusions with >=4 spliced events (remaining=2895)
[2026-06-08T08:55:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1044)
[2026-06-08T08:55:53] Filtering fusions with anchors <=23nt (remaining=839)
[2026-06-08T08:55:53] Filtering end-to-end fusions with low support (remaining=824)
[2026-06-08T08:55:54] Filtering fusions with no coverage around the breakpoints (remaining=811)
[2026-06-08T08:55:55] Indexing gene sequences 
[2026-06-08T08:55:58] Filtering genes with >=30% identity (remaining=268)
[2026-06-08T08:56:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=112)
[2026-06-08T08:56:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=108)
[2026-06-08T08:56:02] Searching for additional isoforms (remaining=125)
[2026-06-08T08:56:04] Assigning confidence scores to events 
[2026-06-08T08:56:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:06] Writing fusions to file 'aih-tih-sc-12b72b-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:07] Writing discarded fusions to file 'aih-tih-sc-12b72b-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:31] Freeing resources
[2026-06-08T08:56:50] Done (elapsed time=00:11:17, CPU time=00:11:15, peak memory=16.5gb)